chr1-159603660-C-T

Variant names:

• chr1-159603660-C-T
• rs6695377

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.332 in 152,046 control chromosomes in the GnomAD database, including 9,754 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (9754 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50483 AN: 151928 Hom.: 9742 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.283

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.332 AC: 50534 AN: 152046 Hom.: 9754 Cov.: 32 AF XY: 0.339 AC XY: 25202 AN XY: 74320

African (AFR) AF: 0.448 AC: 18598 AN: 41472

American (AMR) AF: 0.333 AC: 5094 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3468

East Asian (EAS) AF: 0.835 AC: 4313 AN: 5166

South Asian (SAS) AF: 0.299 AC: 1441 AN: 4812

European-Finnish (FIN) AF: 0.344 AC: 3627 AN: 10552

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15883 AN: 67978

Other (OTH) AF: 0.286 AC: 605 AN: 2116

Alfa AF: 0.252 Hom.: 8627

Bravo AF: 0.338

Asia WGS AF: 0.554 AC: 1921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.41
PhyloP100		-0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6695377; hg19: chr1-159573450;